Dear Ed, since you pointed it out I wonder if there is any reasonable (i.e. w.r.t. data error/ resolution) difference between the interpolated values and the calculated value. I actually doubt that
Cheers, Tim On Fri, Apr 08, 2011 at 12:07:21PM -0400, Ed Pozharski wrote: > Thanks to everyone for their suggestions. The closest solution was > > 1. Expand dataset in P1 using SFTOOLS (keyword EXPAND) > 2. Write it out in text file > (WRITE data.hkl format(3i5,2f16.3) col col1 col2) > 3. Use program HYDENS (Bart Hazes) > > It should be noted that the current version of HYDENS only works in > orthorhombic spacegroups (although there may be a workaround of > pre-calculating fractional coordinates with coordconv and then setting > the unit cell to 1x1x1). > > This was the only solution that actually calculates electron density at > the atomic positions. The rest of options were all to calculate the map > and then interpolate it to the select (x,y,z). Several options exist > for that (in the order they were received): > > 1. MAPMAN (PEEK keyword) (Gerard Kleywegt, James Holton, Edward Berry) > 2. CCTBX (Pavel Afonin) > 3. COOT (density_at_point, probably uses clipper libs) (Paul Emsley) > 4. CHIMERA ("Values at Atom Positions") (Eric Pettersen) > > On Fri, 2011-04-01 at 11:16 -0400, Ed Pozharski wrote: > > I need to calculate the electron density values for a list of spatial > > locations (e.g. atom positions in a model) using an mtz-file that > > already contains map coefficients. To write my own code may be easier > > than I think (if one can manipulate mtz columns, isn't the only problem > > left how to incorporate symmetry-related reflections?), but I would need > > an alternative at least for troubleshooting purposes. So, > > > > Does anyone know of a software tool that can calculate point electron > > density for every atom in a structure? > > > > If I would have to bring a dependency into this, the best choice for me > > would be clipper libs. > > > > Thanks in advance, > > > > Ed. > > > > > > -- > "Hurry up before we all come back to our senses!" > Julian, King of Lemurs -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
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